What is Quarto?

https://quarto.org

Quarto is an open-source scientific and technical publishing system that builds on standard markdown with features essential for scientific communication.

• Computations: Python, R, Julia, Observable JS
• Markdown: Pandoc flavored markdown with many enhancements
• Output: Documents, presentations, websites, books, blogs

Literate programming system in the tradition of Org-Mode, Weave.jl, R Markdown, iPyPublish, Jupyter Book, etc.

Origins

• Open Source project sponsored by Posit, PBC (formerly known as RStudio, PBC)
• 10 years of experience with R Markdown, a similar system that was R-specific, convinced us that the core ideas were sound
• The number of languages and runtimes used for scientific discourse is broad
• Quarto is a ground-up re-imagining of R Markdown that is fundamentally multi-language and multi-engine
• Quarto gets inspiration from both R Markdown and Jupyter, and provides a plain-text option or the use of native Jupyter notebooks

Goal: Computation document

• Documents that include source code for their production
• Notebook AND plain-text flavors
• Programmatic automation and reproducibility

Goal: Scientific Markdown

Goal: Single Source Publishing

Simple Example

---
title: "matplotlib demo"
format:
  html:
    code-fold: true
jupyter: python3
---

For a demonstration of a line plot on a polar 
axis, see @fig-polar.

```{python}
#| label: fig-polar
#| fig-cap: "A line plot on a polar axis"

import numpy as np
import matplotlib.pyplot as plt

r = np.arange(0, 2, 0.01)
theta = 2 * np.pi * r
fig, ax = plt.subplots(
  subplot_kw = {'projection': 'polar'} 
)
ax.plot(theta, r)
ax.set_rticks([0.5, 1, 1.5, 2])
ax.grid(True)
plt.show()
```

Simple Example, multi-format

Can be rendered to dozens of output formats with Quarto (via Pandoc):

quarto render hello.qmd --to html
quarto render hello.qmd --to pdf
quarto render hello.qmd --to docx
quarto render hello.qmd --to epub
quarto render hello.qmd --to pptx
quarto render hello.qmd --to revealjs

So what is Quarto?

Quarto® is an open-source scientific and technical publishing system built on Pandoc.

thomasmock$ quarto --help

Usage:   quarto
Version: 1.2.269

Commands:
  render  [input] [args...] - Render input file(s) to various document types.            
  preview [file] [args...]  - Render and preview a document or website project.          
  publish [provider] [path] - Publish a document or project.

A .qmd is a plain text file

format: html
jupyter: python3

format: html
engine: knitr

```{python}
from siuba import *
(mtcars
  >> group_by(_.cyl)
  >> summarize(avg_mpg = _.mpg.mean()))
```

```{r}
library(dplyr)
mtcars |> 
  group_by(cyl) |> 
  summarize(mean = mean(mpg))
```

# Heading 1
This is a sentence with some **bold text**, some *italic text* and an 
![image](image.png){fig-alt="Alt text for this image"}.

But Quarto doesn’t have to be plain-text

Rendering pipeline

What to do with my existing .ipynb?

# --execute command optional - ignore stored computation
quarto render my-favorite.ipynb --to html --execute

quarto convert --help

Usage:   quarto convert <input>

Description:
    Convert documents to alternate representations.

Convert notebook to markdown:                quarto convert doc.ipynb                
Convert markdown to notebook:                quarto convert doc.qmd                  
Convert notebook to markdown, write to file: quarto convert doc.ipynb --output doc.qmd

nbdev + Quarto = super powers

fast.ai - nbdev+Quarto: A new secret weapon for productivity

Comfort of your own workspace

Auto-completion in RStudio + VSCode

Both RStudio and VSCode with the Quarto extension have rich auto-completion

Interactivity with Jupyter Widgets

import plotly.express as px
import plotly.io as pio
df = px.data.iris()
fig = px.scatter(df, x="sepal_width", y="sepal_length", 
                 color="species", 
                 marginal_y="violin", marginal_x="box", 
                 trendline="ols", template="simple_white")
fig.show()

Interactivity, Observable

Quarto also includes native support for Observable JS, a set of enhancements to vanilla JavaScript created by Mike Bostock (also the author of D3)

viewof bill_length_min = Inputs.range(
  [32, 50], 
  {value: 35, step: 1, label: "Bill length (min):"}
)
viewof islands = Inputs.checkbox(
  ["Torgersen", "Biscoe", "Dream"], 
  { value: ["Torgersen", "Biscoe"], 
    label: "Islands:"
  }
)

Plot.rectY(filtered, 
  Plot.binX(
    {y: "count"}, 
    {x: "body_mass", fill: "species", thresholds: 20}
  ))
  .plot({
    facet: {
      data: filtered,
      x: "sex",
      y: "species",
      marginRight: 80
    },
    marks: [
      Plot.frame(),
    ]
  }
)

Inputs.table(filtered)

data = FileAttachment("palmer-penguins.csv").csv({ typed: true })

filtered = data.filter(function(penguin) {
  return bill_length_min < penguin.bill_length &&
         islands.includes(penguin.island);
})

Quarto, also with Observable Javascript!

viewof temp = Inputs.range([0, 100], {step: 1, value: 34, label: htl.html`Temp ℃`})

```{ojs}
viewof temp = Inputs.range([0, 100], {step: 1, value: 34, label: htl.html`Temp ℃`})
```

Converting temperature from &#x2103; to &#x2109; <br>  
Celsius = ${d3.format(".0f")(temp)}&#x2103; and Fahrenheit = ${d3.format(".1f")(temp * 9/5 + 32)}&#x2109;.

Quarto, unified document layout

quarto render boston-terrier.qmd --to html

quarto render boston-terrier.qmd --to pdf